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<a href="Alignment_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00028"></a>00028 <span class="preprocessor">#ifndef MOLTK_ALIGN_ALIGNMENT_H</span>
<a name="l00029"></a>00029 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_ALIGN_ALIGNMENT_H</span>
<a name="l00030"></a>00030 <span class="preprocessor"></span>
<a name="l00031"></a>00031 <span class="preprocessor">#include &quot;<a class="code" href="EString_8hpp.html" title="EString class compact representation of aligned sequence gap structure.">moltk/EString.hpp</a>&quot;</span>
<a name="l00032"></a>00032 <span class="preprocessor">#include &quot;<a class="code" href="PDBStructure_8hpp.html" title="Macromolecular atomic structure classes.">moltk/PDBStructure.hpp</a>&quot;</span>
<a name="l00033"></a>00033 <span class="preprocessor">#include &quot;<a class="code" href="units_8hpp.html" title="templated Dimension, Unit, and Quantity classes for type safe scientific dimensional analysis and com...">moltk/units.hpp</a>&quot;</span>
<a name="l00034"></a>00034 
<a name="l00035"></a>00035 <span class="keyword">namespace </span>moltk {
<a name="l00036"></a>00036 
<a name="l00040"></a>00040 <span class="keyword">template</span>&lt;<span class="keyword">class</span> SCORE_TYPE&gt;
<a name="l00041"></a><a class="code" href="classmoltk_1_1Alignment__.html">00041</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>
<a name="l00042"></a>00042 {
<a name="l00043"></a>00043 <span class="keyword">public</span>:
<a name="l00044"></a>00044 
<a name="l00045"></a>00045 
<a name="l00047"></a><a class="code" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8">00047</a>     <span class="keyword">enum</span> <a class="code" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8" title="Whether a particular Alignment_ member is a sequence or structure.">List</a> {
<a name="l00048"></a><a class="code" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8a3a38c67cfd20916ed2aca72d487e4eb8">00048</a>         <a class="code" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8a3a38c67cfd20916ed2aca72d487e4eb8" title="Item belongs to the sequence list.">LIST_SEQUENCE</a>, 
<a name="l00049"></a><a class="code" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8aed118ee80047d7db2b9148f435540686">00049</a>         <a class="code" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8aed118ee80047d7db2b9148f435540686" title="Item belongs to the structure list.">LIST_STRUCTURE</a> 
<a name="l00050"></a>00050     };
<a name="l00051"></a>00051 
<a name="l00052"></a><a class="code" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">00052</a>     <span class="keyword">typedef</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">moltk::EString</a> <a class="code" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a>;
<a name="l00053"></a>00053 
<a name="l00055"></a><a class="code" href="classmoltk_1_1Alignment___1_1Row.html">00055</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1Alignment___1_1Row.html" title="Meta-data for one sequence in an Alignment_.">Row</a>
<a name="l00056"></a>00056     {
<a name="l00057"></a>00057     <span class="keyword">public</span>:
<a name="l00058"></a><a class="code" href="classmoltk_1_1Alignment___1_1Row.html#ab797eb0dfbf30a2db2e2f3673aee5bf6">00058</a>         <a class="code" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8" title="Whether a particular Alignment_ member is a sequence or structure.">List</a> <a class="code" href="classmoltk_1_1Alignment___1_1Row.html#ab797eb0dfbf30a2db2e2f3673aee5bf6" title="which list: sequences or structures?">list</a>; 
<a name="l00059"></a><a class="code" href="classmoltk_1_1Alignment___1_1Row.html#a40eec6b995d925971d17c072dbf03998">00059</a>         <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1Alignment___1_1Row.html#a40eec6b995d925971d17c072dbf03998" title="index into either the structure or sequence list">list_index</a>; 
<a name="l00060"></a><a class="code" href="classmoltk_1_1Alignment___1_1Row.html#a655f1804f8dd752f58c3c8c9ba0349c0">00060</a>         <a class="code" href="namespacemoltk.html#afe6fbd8f5686b34143c2742fcc97292c" title="Real represents a real number, such as 5.6.">Real</a> <a class="code" href="classmoltk_1_1Alignment___1_1Row.html#a655f1804f8dd752f58c3c8c9ba0349c0" title="relative contribution of this sequence to the alignment score">sequence_weight</a>; 
<a name="l00061"></a><a class="code" href="classmoltk_1_1Alignment___1_1Row.html#a9d30e8fb78dcfa20b626c9055e3e6c49">00061</a>         <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a> <a class="code" href="classmoltk_1_1Alignment___1_1Row.html#a9d30e8fb78dcfa20b626c9055e3e6c49" title="gap pattern of this sequence">e_string</a>; 
<a name="l00062"></a>00062     };
<a name="l00063"></a>00063 
<a name="l00064"></a>00064 
<a name="l00065"></a>00065 <span class="keyword">public</span>:
<a name="l00067"></a>00067     <a class="code" href="classmoltk_1_1Alignment__.html#af92538fd947d2503ecd35984642b875c" title="Default constructor creates an empty Alignment_.">Alignment_</a>();
<a name="l00069"></a>00069     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment__.html#af92538fd947d2503ecd35984642b875c" title="Default constructor creates an empty Alignment_.">Alignment_</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; sequence);
<a name="l00071"></a>00071     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment__.html#af92538fd947d2503ecd35984642b875c" title="Default constructor creates an empty Alignment_.">Alignment_</a>(<span class="keyword">const</span> std::string&amp; alignment_string);
<a name="l00073"></a>00073     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment__.html#af92538fd947d2503ecd35984642b875c" title="Default constructor creates an empty Alignment_.">Alignment_</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* alignment_string);
<a name="l00075"></a><a class="code" href="classmoltk_1_1Alignment__.html#a96e7fab5bcacdb8c9f1fa2b272cd3dc2">00075</a>     <a class="code" href="classmoltk_1_1Alignment__.html#a96e7fab5bcacdb8c9f1fa2b272cd3dc2" title="Delete alignment (destructor)">~Alignment_</a>() {}
<a name="l00077"></a>00077     <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>&amp; <a class="code" href="classmoltk_1_1Alignment__.html#a6aa429375949cd6c7fd4b58960afcc7b" title="Add one sequence to the alignment. Internally, gaps will be removed and encoded into an EString...">append_sequence</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; sequence);
<a name="l00079"></a>00079     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment__.html#a685b48576e005de9013fea1c1457814c" title="Add sequences from fasta sequences or a single sequence string.">load_string</a>(<span class="keyword">const</span> std::string&amp; alignment_string);
<a name="l00081"></a>00081     <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>&amp; <a class="code" href="classmoltk_1_1Alignment__.html#abfd24b91e6307001f8268a8b95a78fb1" title="Load fasta format sequences from a C++ stream.">load_fasta</a>(std::istream&amp; input_stream);
<a name="l00083"></a>00083     <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>&amp; <a class="code" href="classmoltk_1_1Alignment__.html#abfd24b91e6307001f8268a8b95a78fb1" title="Load fasta format sequences from a C++ stream.">load_fasta</a>(<span class="keyword">const</span> std::string&amp; file_name);
<a name="l00084"></a>00084 
<a name="l00086"></a>00086     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment__.html#a530d9e4e4b1c3d1334d6db811a299f10" title="Write a pretty formatted alignment to a C++ stream.">write_pretty</a>(std::ostream&amp; output_stream) <span class="keyword">const</span>;
<a name="l00088"></a>00088     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment__.html#a530d9e4e4b1c3d1334d6db811a299f10" title="Write a pretty formatted alignment to a C++ stream.">write_pretty</a>(<span class="keyword">const</span> std::string&amp; file_name) <span class="keyword">const</span>;
<a name="l00090"></a>00090     std::string <a class="code" href="classmoltk_1_1Alignment__.html#ada1e80499e1d31106f1b319f233b3c60" title="Create a string containing a pretty formatted alignment.">pretty</a>() <span class="keyword">const</span>;
<a name="l00091"></a>00091 
<a name="l00093"></a>00093     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment__.html#ae92aea8bd71e9af1918cebda993da208" title="Write Alignment_ in fasta format to a C++ stream.">write_fasta</a>(std::ostream&amp; output_stream) <span class="keyword">const</span>;
<a name="l00095"></a>00095     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment__.html#ae92aea8bd71e9af1918cebda993da208" title="Write Alignment_ in fasta format to a C++ stream.">write_fasta</a>(<span class="keyword">const</span> std::string&amp; file_name) <span class="keyword">const</span>;
<a name="l00097"></a>00097     std::string <a class="code" href="classmoltk_1_1Alignment__.html#a64ffedc0eba04a1a80c349a757275b35" title="Create a string with Alignment_ in fasta format.">fasta</a>() <span class="keyword">const</span>;
<a name="l00098"></a>00098 
<a name="l00100"></a>00100     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment__.html#a3e3b0dbdb6593e6446ea92a21f5af53c" title="Write table of pairwise sequence identities to a C++ stream.">write_id_table</a>(std::ostream&amp; output_stream) <span class="keyword">const</span>;
<a name="l00102"></a>00102     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment__.html#a3e3b0dbdb6593e6446ea92a21f5af53c" title="Write table of pairwise sequence identities to a C++ stream.">write_id_table</a>(<span class="keyword">const</span> std::string&amp; file_name) <span class="keyword">const</span>;
<a name="l00104"></a>00104     std::string <a class="code" href="classmoltk_1_1Alignment__.html#a03fb9aaf5c82353cb7152364542654d9" title="Create a string containing table of pairwise sequence identities.">id_table</a>() <span class="keyword">const</span>;
<a name="l00105"></a>00105 
<a name="l00107"></a>00107     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Alignment__.html#ac113e59bf55f00ffd7957a39b0d13f5c" title="Number of columns (width) of sequence Alignment_.">get_number_of_columns</a>() <span class="keyword">const</span>;
<a name="l00109"></a><a class="code" href="classmoltk_1_1Alignment__.html#a53d9faa384258178abd19592740deda6">00109</a>     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Alignment__.html#a53d9faa384258178abd19592740deda6" title="get_number_of_sequences() includes combined number of both sequences and structures">get_number_of_sequences</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Alignment__.html#a468e2e5c2a46fb3b163805942a533c08">rows</a>.size();}
<a name="l00110"></a>00110 
<a name="l00115"></a>00115     <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> <a class="code" href="classmoltk_1_1Alignment__.html#a1cf784f435f461b69d2cb6fed194e1c8" title="Align two sequence alignments using a pair of precomputed EStrings.">align</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>&amp;, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp;, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp;) <span class="keyword">const</span>;
<a name="l00116"></a>00116 
<a name="l00118"></a>00118     <span class="keyword">const</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures.">BaseBiosequence</a>&amp; <a class="code" href="classmoltk_1_1Alignment__.html#a3320970bfee0ea1058c5a75632fa56b0" title="Returns the particular sequence or structure at Row index.">get_sequence</a>(<span class="keywordtype">size_t</span> index) <span class="keyword">const</span>;
<a name="l00120"></a>00120     <span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp; <a class="code" href="classmoltk_1_1Alignment__.html#a3408c640ccc854b0b9af7a593521186a" title="The gapping pattern of Row index.">get_estring</a>(<span class="keywordtype">size_t</span> index) <span class="keyword">const</span>;
<a name="l00122"></a>00122     <span class="keyword">const</span> SCORE_TYPE&amp; <a class="code" href="classmoltk_1_1Alignment__.html#a14c87e3b0fbf3fc6ddaffb74f18aa539" title="The precomputed total sum of pairs score of this Alignment_.">get_score</a>() <span class="keyword">const</span>;
<a name="l00124"></a>00124     <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>&amp; <a class="code" href="classmoltk_1_1Alignment__.html#a42cec9b9709afe53383953f3f687d16c" title="Set the sum of pairs score for this Alignment_. Make sure you put the correct answer!">set_score</a>(<span class="keyword">const</span> SCORE_TYPE&amp; s);
<a name="l00126"></a>00126     std::string <a class="code" href="classmoltk_1_1Alignment__.html#a825baa50931639decf5b6989801412f2" title="Low level python string representation of this Alignment_.">repr</a>() <span class="keyword">const</span>;
<a name="l00127"></a><a class="code" href="classmoltk_1_1Alignment__.html#a0a7ba36b2af5bc886e8bcbc4fbdb4400">00127</a>     <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>&amp; <a class="code" href="classmoltk_1_1Alignment__.html#a0a7ba36b2af5bc886e8bcbc4fbdb4400">set_pretty_width</a>(<span class="keywordtype">int</span> width) {<a class="code" href="classmoltk_1_1Alignment__.html#a7b353afe4712a512a87f5ef9e61af88c">pretty_width</a> = width; <span class="keywordflow">return</span> *<span class="keyword">this</span>;}
<a name="l00128"></a><a class="code" href="classmoltk_1_1Alignment__.html#aefff61528a8a3210501ee4e517c485b6">00128</a>     <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1Alignment__.html#aefff61528a8a3210501ee4e517c485b6">get_pretty_width</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Alignment__.html#a7b353afe4712a512a87f5ef9e61af88c">pretty_width</a>;}
<a name="l00129"></a><a class="code" href="classmoltk_1_1Alignment__.html#a8618745ccb54c7588fa56cfc1f264d3a">00129</a>     <span class="keyword">inline</span> <span class="keyword">friend</span> std::ostream&amp; operator&lt;&lt;(std::ostream&amp; os, const moltk::Alignment_&lt;SCORE_TYPE&gt;&amp; ali) {
<a name="l00130"></a>00130         ali.write_pretty(os);
<a name="l00131"></a>00131         <span class="keywordflow">return</span> os;
<a name="l00132"></a>00132     }
<a name="l00133"></a>00133 
<a name="l00134"></a>00134 <span class="keyword">protected</span>:
<a name="l00135"></a><a class="code" href="classmoltk_1_1Alignment__.html#afb22dd1d74614d10f0633ce8bfb2f6a6">00135</a>     std::vector&lt;Biosequence&gt; <a class="code" href="classmoltk_1_1Alignment__.html#afb22dd1d74614d10f0633ce8bfb2f6a6">sequences</a>;
<a name="l00136"></a><a class="code" href="classmoltk_1_1Alignment__.html#ab7ef21f5246cf6aeeb64e199d02ff8fa">00136</a>     std::vector&lt;PDBStructure::Chain&gt; <a class="code" href="classmoltk_1_1Alignment__.html#ab7ef21f5246cf6aeeb64e199d02ff8fa">structures</a>;
<a name="l00137"></a><a class="code" href="classmoltk_1_1Alignment__.html#a468e2e5c2a46fb3b163805942a533c08">00137</a>     std::vector&lt;Row&gt; <a class="code" href="classmoltk_1_1Alignment__.html#a468e2e5c2a46fb3b163805942a533c08">rows</a>;
<a name="l00138"></a><a class="code" href="classmoltk_1_1Alignment__.html#ac929115e5fbbfb6a16f537f0d024ff72">00138</a>     SCORE_TYPE <a class="code" href="classmoltk_1_1Alignment__.html#ac929115e5fbbfb6a16f537f0d024ff72">m_score</a>;
<a name="l00139"></a><a class="code" href="classmoltk_1_1Alignment__.html#a7b353afe4712a512a87f5ef9e61af88c">00139</a>     <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1Alignment__.html#a7b353afe4712a512a87f5ef9e61af88c">pretty_width</a>;
<a name="l00140"></a>00140 };
<a name="l00141"></a>00141 
<a name="l00142"></a><a class="code" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">00142</a> <span class="keyword">typedef</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_&lt;moltk::units::Information&gt;</a> <a class="code" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a>;
<a name="l00143"></a>00143 
<a name="l00145"></a>00145 <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> <a class="code" href="namespacemoltk.html#a5d6a32006fb76447d32cde962b6ab1fb" title="global load_fasta method helps get SEQUOIA-like conciseness in python.">load_fasta</a>(<span class="keyword">const</span> std::string&amp; file_name);
<a name="l00146"></a>00146 
<a name="l00147"></a>00147 } <span class="comment">// namespace moltk</span>
<a name="l00148"></a>00148 
<a name="l00149"></a>00149 
<a name="l00150"></a>00150 <span class="preprocessor">#endif // MOLTK_ALIGN_ALIGNMENT_H</span>
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